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The structure of glutathione, γ-l-Glutamyl-l-cysteinyl-glycine (C10H17N3O6S), was studied by multi-temperature single-crystal X-ray diffraction. Residual density maps from conventional independent atom model refinement gave indication of anharmonic motion in the molecule. This was further investigated by invariom refinement with anisotropic displacement parameters for all atoms, which described asphericity due to chemical bonding and lone pairs; afterwards only the residual-density signal of anharmonic motion remained. Treating anharmonicity with third-order Gram-Charlier displacement parameters led to regions with unphysical negative electron density. In contrast, a maximum entropy method (MEM) determination of the electron density successfully takes the features into account. Respective difference electron density plots (MEM minus prior and [Invariom+GC] minus invariom) agree well with each other. Challenges in treating and understanding the phenomenon are discussed. A procedure is proposed how unphysical negative electron density can be avoided. It is closely related to the free lunch algorithm. [ABSTRACT FROM AUTHOR]

Crown ethers and their supramolecular derivatives are well-known chelators and scavengers for a variety of cations, most notably heavier alkali and alkaline-earth ions. Although they are widely used in synthetic chemistry, available crystal structures of uncoordinated and solvent-free crown ethers regularly suffer from disorder. In this study, we present the X-ray crystal structure analysis of well-ordered solvent-free crystals of dibenzo-21-crown-7 (systematic name: dibenzo[ b, k]-1,4,7,10,13,16,19-heptaoxacycloheneicosa-2,11-diene, C22H28O7). Because of the quality of the crystal and diffraction data, we have chosen invarioms, in addition to standard independent spherical atoms, for modelling and briefly discuss the different refinement results. The electrostatic potential, which is directly deducible from the invariom model, and the Hirshfeld surface are analysed and complemented with interaction-energy computations to characterize intermolecular contacts. The boat-like molecules stack along the a axis and are arranged as dimers of chains, which assemble as rows to form a three-dimensional structure. Dispersive C-H...H-C and C-H...π interactions dominate, but nonclassical hydrogen bonds are present and reflect the overall rather weak electrostatic influence. A fingerprint plot of the Hirshfeld surface summarizes and visualizes the intermolecular interactions. The insight gained into the crystal structure of dibenzo-21-crown-7 not only demonstrates the power of invariom refinement, Hirshfeld surface analysis and interaction-energy computation, but also hints at favourable conditions for crystallizing solvent-free crown ethers. [ABSTRACT FROM AUTHOR]

Two new polymorphs of the phase-change material sodium acetate were characterized by single-crystal X-ray diffraction. A tetragonal form was found first. It converted to a orthorhombic form after measurement of a single crystal of the tetragonal form at 100 K and subsequent warming to ambient temperature. Hirshfeld surface fingerprint plots show the different packing environments of the two new compared to the two known orthorhombic polymorphs Forms I and II. The accuracy and precision of the structures were improved compared to conventional independent atom model refinement through the use of aspherical scattering factors of the invariom database. We think that the layered nature of all sodium acetate forms, and the thereby limited (“quantized”) availability of vibrational modes, is related to the phenomenon of supersaturation, which is connected to its phase-change properties.

The temperature dependence of H- Uiso in N-acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H- Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found. [ABSTRACT FROM AUTHOR]

A new monoclinic solvate containing two molecules of the thiopeptide antibiotic thiostrepton in the asymmetric unit has been crystallized in space group P21. Single-crystal diffraction data to a resolution of 0.64 Å were collected at the SLS synchrotron, allowing structure solution by direct methods and resolution of the disorder present. Valence electron density can be observed in the Fourier residual density from refinement with the independent-atom model, which is a prerequisite for successful application of more sophisticated aspherical-atom scattering factors such as the invariom model when aiming to improve the structural model. Invariom refinement improves quality indicators such as R1( F) for thiostrepton, as previously demonstrated for small molecules. The nonspherical electron-density model also allows the direct derivation of a dipole moment and an electrostatic potential for the whole molecule, which is discussed in the context of antibiotic activity and molecular recognition. [ABSTRACT FROM AUTHOR]

Two new polymorphs of the phase-change material sodium acetate were characterized by single-crystal X-ray diffraction. A tetragonal form was found first. It converted to a orthorhombic form after measurement of a single crystal of the tetragonal form at 100 K and subsequent warming to ambient temperature. Hirshfeld surface fingerprint plots show the different packing environments of the two new compared to the two known orthorhombic polymorphs Forms I and II. The accuracy and precision of the structures were improved compared to conventional independent atom model refinement through the use of aspherical scattering factors of the invariom database. We think that the layered nature of all sodium acetate forms, and the thereby limited (“quantized”) availability of vibrational modes, is related to the phenomenon of supersaturation, which is connected to its phase-change properties. [ABSTRACT FROM AUTHOR]

The temperature dependence of H-U(iso) in N-acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U(iso) below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.